Abstract
AbstractEnvironmental DNA (eDNA) has rapidly emerged as a promising biodiversity monitoring technique, proving to be a sensitive and cost‐effective method for species detection. Despite the increasing popularity of eDNA, several questions regarding its limitations remain to be addressed. We investigated the effect of sampling medium and time, and preservation methods, on fish detection performance based on eDNA metabarcoding of neotropical freshwater samples. Water and sediment samples were collected from 11 sites along the Jequitinhonha River, Southeastern Brazil; sediment samples were stored in ethanol, while the same amounts of water per sample (3 L) were stored in a cool box with ice, as well as by adding the cationic surfactant benzalkonium chloride (BAC). Sediment and water samples yielded a similar amount of fish MOTUs (237 vs. 239 in the first sampling event, and 153 vs. 142 in the second sampling event). Water stored in ice provided better results than those preserved in BAC (239 and 142 vs. 194 and 71 MOTUs). While documenting the effectiveness of eDNA surveys as practical tools for fish biodiversity monitoring in poorly accessible areas, we showed that keeping water samples cooled results in greater eDNA recovery and taxon detection than by adding cationic surfactants (BAC) as sample preservatives. Furthermore, by comparing two sets of samples collected from the same locations at a 3‐week interval, we highlight the importance of conducting multiple sampling events when attempting to recover a realistic picture of fish assemblages in lotic systems.
Highlights
Environmental DNA metabarcoding has been hailed as a promising tool for biodiversity assessment and monitoring worldwide, in both marine and freshwater ecosystems (Bohmann et al, 2014; Boussarie et al, 2018; Deiner et al, 2017; Hänfling et al, 2016; Pont et al., 2018; Thomsen & Willerslev, 2015)
Despite the exponential increase of Environmental DNA (eDNA) publications, most of the studies have been conducted in temperate regions and in fairly well accessible areas
Few studies have tested the use of eDNA metabarcoding in remote tropical sites, and to our knowledge no study encompassing freshwater fish biodiversity at a large scale has been performed in Brazil
Summary
Environmental DNA metabarcoding has been hailed as a promising tool for biodiversity assessment and monitoring worldwide, in both marine and freshwater ecosystems (Bohmann et al, 2014; Boussarie et al, 2018; Deiner et al, 2017; Hänfling et al, 2016; Pont et al., 2018; Thomsen & Willerslev, 2015). A rapid removal of eDNA (through transport and degradation) might hamper the detec‐ tion of species and lead to false negatives (Hansen et al, 2018), com‐ promising the use of this method for biodiversity assessment and monitoring. In this context, testing effectiveness of sampling meth‐ ods is important in remote and tropical locations (Ladell et al, 2018). We obtained water and sediment samples from 11 sites located along the main stem of River Jequitinhonha (South‐Eastern Brazil), and: (a) compared two preservation methods for water samples (cooling the samples using ice and adding the cationic surfactant Benzalkonium chloride—BAC); (b) compared MOTU recovery from water versus sediment samples; and (c) examined the influence of short‐term temporal sample replication by sampling the same locations over a 3‐week interval
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