Influence of preservation methods, sample medium and sampling time on eDNA recovery in a neotropical river

Environmental 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 me‐ dium and time, and preservation
methods, on fish detection performance based on eDNA metabarcoding of
neotropical freshwater samples. Water and sediment sam‐ ples were
collected from 11 sites along the Jequitinhonha River, Southeastern
Brazil; sediment samples were stored in ethanol, while the same amounts of
water per sam‐ ple (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 pre‐ servatives. 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.