Species detection from aquatic eDNA: Assessing the importance of capture methods

Abstract

Environmental DNA (eDNA) is increasingly used for biodiversity monitoring, particularly in aquatic systems. However, each step, from sample collection to bioinformatic analysis, can introduce biases and influence the reliability of results. While much effort has been put into the optimization of laboratory methods, less attention has been devoted to estimate the impacts of eDNA capture methods. To address this issue, water samples were collected at nine small ponds and puddles where up to 10 amphibian species occur, using precipitation, disc filters, and capsules. We focused on targeted detection of an amphibian species, Salamandra salamandra, and on the composition of the whole amphibian community. Species detection was performed using a novel qPCR assay for S. salamandra and high‐throughput sequencing, combined with stringent versus relaxed PCR replication thresholds. Filtration techniques (disc filters and capsules) outperformed precipitation, generating a higher number of detections of S. salamandra and higher amounts of captured eDNA, while species detection was identical between disc filters and capsules. There were no significant differences between capture methods regarding amphibian community composition. The variation in detection success associated with capture methods was far higher than that associated with PCR replication, regardless of the detection method used. Our results highlight the importance of choosing a suitable capture method for eDNA studies and suggest that the choice of capture method outweighs the choice of detection method used. To the best of our knowledge, this is the first study to compare high‐capacity capsules with common eDNA methods for water samples, such as precipitation and standard disc filters.

Navigating the trade‐offs between environmental DNA and conventional field surveys for improved amphibian monitoring

“…Studies that directly compare methods across multiple axes of variation (e.g., species, season, sampling protocol) are essential for optimizing eDNA surveys. For example, although still comparatively rare, direct comparisons of qPCR and metabarcoding, especially those incorporating multiple species or sampling protocols, can inform the choice of technique for specific applications (Blackman et al, 2020; Bylemans et al, 2019; Deiner et al, 2017; Dritsoulas et al, 2020; Harper et al, 2018; Lacoursière‐Roussel et al, 2016; Peixoto et al, 2021; Schneider et al, 2016). In addition, explicitly quantifying the mechanisms shaping detection probability (rather than using a descriptive approach to compare detections across protocols, environments, or species) provides concrete information for further refining eDNA survey methods (Fediajevaite et al, 2021; Willoughby et al, 2016).…”

Speeding up the detection of invasive bivalve species using environmental DNA: A Nanopore and Illumina sequencing comparison

“…Rather, we compared a MinION protocol that appeared to be working well in our laboratory at CIBIO-InBIO (Portugal) with an Illumina protocol that has been used in numerous studies (Egeter et al, 2018;Martins et al, 2021;Mata et al, 2021;Peixoto et al, 2021).…”

Development of Quantitative Real-Time PCR for Detecting Environmental DNA Derived from Marine Macrophytes and Its Application to a Field Survey in Hiroshima Bay, Japan

“…Hamaguchi et al [27] also used amplicons of 90 bp and 102 bp for the ITS and matK regions, respectively, which are different in length. Peixoto et al [17] pointed out that different amplicon sizes may cause differences in the degradation process. Therefore, the amplicon size should be the same when making comparisons, whether this is because of the length of both PCR products or because the number of copies of each DNA in the cell or the location of each DNA must be clarified through studies using experimental degradation of eelgrass.…”

“…Two eDNA techniques are presently used to investigate organic carbon in marine sediments: comparative metabarcoding using next-generation sequencing (NGS), and species-specific analysis using quantitative realtime PCR (qPCR). A few studies to date have directly compared these methods of eDNA detection, describing the advantages and disadvantages of each method [15][16][17].…”