Environmental DNA monitoring and management of invasive fish: comparison of eDNA and fyke netting

Abstract

Harbours are known introduction foci of marine alien species. They act as recipients of new introductions and as sources for regional spread. We report on subtidal surveys of fouling communities from 14 harbours along the coastline of South Africa that were used to identify predictors of high alien species numbers in support of prioritisation of monitoring actions by authorities. The harbours varied in nature from large, international shipping hubs to small, regional fishing harbours and recreational marinas. Fouling assemblages were assessed using visual and scrape sampling to ensure the detection of large, mobile and small inconspicuous species. In total, 29 alien species were recorded, 15 of which were detected outside of their previously known ranges. The number of species recorded per harbour varied from five to. Results revealed that high numbers of alien species were associated with the presence of yachts and low primary productivity. Harbours which had yachts and occurred in areas with mean Chl a minimum levels lower than 0.21 mg.m-3 had the highest number of alien species, while harbours without yachts that were larger than 0.1km 2 supported the fewest alien species. These findings suggest that the presence of yachts can be used to identify harbours with high numbers of alien species, particularly in regions with low productivity. While the applicability of these findings to other regions remains to be tested, this work suggests that harbours that fall within this category could be prioritised for monitoring of marine alien species.

Development and application of environmental DNA surveillance for the threatened crucian carp (Carassius carassius)

“…We sampled five 2 L water samples from each pond in autumn 2016, but timing and/or sampling effort may have been inappropriate. A seasonal effect on common carp eDNA detection was observed, where spring sampling generated higher eDNA concentration and detection rates due to greater common carp activity (Turner et al., ) and density (Hinlo, Furlan, Suitor, & Gleeson, ). As water sampling did not coincide with fyke netting (spring 2016) in our study, eDNA concentration may not reflect CPUE estimates.…”

“…We performed a 10‐fold serial dilution of the gBlocks ® fragment to generate a six‐point standard curve that ranged from 10 6 to 10 copies/μl. eDNA samples were compared to these known concentrations for quantification (Hinlo, Furlan, Suitor, & Gleeson, ). Each standard was replicated five times on each qPCR plate.…”

“…Primarily, crucian carp are surveyed using fyke netting or electrofishing, but these methods can be costly and time‐consuming. Environmental DNA (eDNA) analysis offers a potentially rapid and cost‐effective approach to fish monitoring (Hänfling et al., ; Hinlo, Furlan, Suitor, & Gleeson, ; Jerde, Mahon, Chadderton, & Lodge, ; Sigsgaard, Carl, Møller, & Thomsen, ; Wilcox et al., ). Species are identified using DNA deposited in the environment by individuals via secretions, excretions, gametes, blood, or decomposition (Lawson Handley, ).…”

“…However, these estimates can be inconsistent across habitats and target organisms. In flowing water, Hinlo, Furlan, Suitor, and Gleeson () found no relationship between DNA copy number and conventional density estimates of common carp, yet Takahara, Minamoto, Yamanaka, Doi, and Kawabata () observed a positive association between common carp biomass and eDNA concentration in ponds. Environmental variables play a substantial role in abundance/biomass estimation by influencing the ecology of eDNA (Barnes et al., ).…”

Environmental DNA Sampling of Small‐Bodied Minnows: Performance Relative to Location, Species, and Traditional Sampling

“…), but in others the relationship is unclear (Hinlo et al. ), likely because of sampling techniques (Wilcox et al. ), environmental conditions, and physiological processes of the study organisms.…”