Improving the detection of rare native fish species in environmental DNA metabarcoding surveys

Abstract

The presence of threatened or endangered species often strongly influences management and conservation decisions. Within the Murray–Darling Basin (MDB), Australia, the presence of threatened native fish affects the management and allocation of water resources. In New South Wales, these decisions are currently based on traditional fisheries data and a predictive MaxEnt model. However, it is important to verify the model's predictive power given the implication it may have, but this requires methods with a high detection sensitivity for rare species. Although the use of environmental DNA (eDNA) monitoring, in particular eDNA metabarcoding, achieves a higher detection sensitivity compared with traditional methods, earlier surveys in the MDB have shown that the highly abundant and invasive common carp (Cyprinus carpio) can reduce detection probabilities for rare species. Consequently, a polymerase chain reaction (PCR) blocking primer designed to block the amplification of carp eDNA could increase the detection probabilities for rare native species while simultaneously reducing the required sampling effort and survey costs. Although PCR blocking primers are often used in ancient DNA and dietary studies, no aquatic eDNA metabarcoding study to date has evaluated the potential benefits of using PCR blocking primers. A laboratory and field‐based pilot study was used to address this knowledge gap and assess the impact of a blocking primer, targeting cyprinid fishes (including carp), on the detection probabilities of native species and the minimum sampling effort required. Results showed that the inclusion of the blocking primer increased the detection probabilities for native species by 10–20% and reduced the minimum required sampling effort by 25–50%. These findings provide important insights into possible methods for optimizing eDNA metabarcoding surveys for the detection of rare aquatic species.

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

“…Testing primers in vitro would further elucidate the mechanisms underlying false negatives. In practice, more taxon‐specific primers (e.g., Bálint et al, 2018; Valentini et al, 2016), blocking primers (Rojahn et al, 2021), or additional primer sets targeting different genetic markers (Collins et al, 2019) could be used to enhance the detection of focal taxa relative to other vertebrates.…”

Revisiting the effect of PCR replication and sequencing depth on biodiversity metrics in environmental DNA metabarcoding

“…They found that curves began to flatten only after this relatively higher level of replication and predicted that species accumulation would plateau with 10–20 replicates. More recently, Rojahn et al ( 2021 ), while exploring the effect of PCR replication for detecting rare species of fish, suggested that high PCR replication is not sufficient in some cases to detect rare taxa, in particular where common taxa may swamp the PCR and inhibit detection.…”

Ferries and Environmental DNA: Underway Sampling From Commercial Vessels Provides New Opportunities for Systematic Genetic Surveys of Marine Biodiversity

“…Similarly, bowhead whale (Balaena mysticetus) eDNA was found to diminish substantially in water samples collected as little as 10 min after the whale presence (Székely et al, 2021). The reported challenges in detecting cetacean eDNA suggest that the results from our pilot study using novel primers optimized to for cetaceans are encouraging (Valsecchi et al, 2020), given that a) they allow for amplification of all vertebrate taxa, meaning low-prevalence eDNA could be overwhelmed by high abundance targets (Rojahn et al, 2021); and b) metabarcoding is less sensitive to detecting rare signals than species specific qPCR assays (Harper et al, 2018;Qu and Stewart, 2019).…”