Monitoring of environmental DNA from nonindigenous species of algae, dinoflagellates and animals in the North East Atlantic

Steen Wilhelm Knudsen,Martin Hesselsøe,Jens Thaulow,Sune Agersnap,Brian Klitgaard Hansen,Magnus Wulff Jacobsen,Dorte Bekkevold,Søren K.S Jensen,Peter Rask Møller,Jesper H Andersen

doi:10.1016/j.scitotenv.2022.153093

Abstract

Monitoring the distribution of marine nonindigenous species is a challenging task. To support this monitoring, we developed and validated the specificity of 12 primer-probe assays for detection of environmental DNA (eDNA) from marine species, all nonindigenous to Europe. The species include sturgeons, a Pacific red algae, oyster thief, a freshwater hydroid from the Black Sea, Chinese mitten crab, Pacific oyster, warty comb jelly, sand gaper, round goby, pink salmon, rainbow trout and North American mud crab. We tested all assays in the laboratory, on DNA extracted from both the target and non-target species to ensure that they only amplified DNA from the intended species. Subsequently, all assays were used to analyse water samples collected at 16 different harbours across two different seasons during 2017. We also included six previously published assays targeting eDNA from goldfish, European carp, two species of dinoflagellates of the genera Karenia and Prorocentrum, two species of the heterokont flagellate genus Pseudochattonella. Conventional monitoring was carried out alongside eDNA sampling but with only one sampling event over the one year. Because eDNA was relatively fast and easy to collect compared to conventional sampling, we sampled eDNA twice during 2017, which showed seasonal changes in the distribution of nonindigenous species. Comparing eDNA levels with salinity gradients did not show any correlation. A significant correlation was observed between number of species detected with conventional monitoring methods and number of species found using eDNA at each location. This supports the use of eDNA for surveillance of the distribution of marine nonindigenous species, where the speed and relative easy sampling in the field combined with fast molecular analysis may provide advantages compared to conventional monitoring methods. Prior validation of assays increases taxonomic precision, and laboratorial setup facilitates analysis of multiple samples simultaneously. The specific eDNA assays presented here can be implemented directly in monitoring programmes across Europe and potentially worldwide to infer a more precise picture of the dynamics in the distribution of marine nonindigenous species.

Highlights

We focus on Nonindigenous species (NIS) that mainly are a concern for North European seas, such as the Chinese mitten crab (Eriocheir sinensis), the sand gaper (Mya arenaria) and oyster thief or bulb seaweed (Colpomenia peregrina) (Gofas et al, 2001; Green et al, 2012; Herborg et al, 2005; Køie and Kristiansen, 2000)
Once the assays were applied on water samples, the environmental DNA (eDNA) monitoring turned out to be capable of supporting the conventional monitoring (Figs. 2–3, Table 6)
Our results show that eDNA monitoring has not reached a level where it can completely replace conventional monitoring

Summary

Introduction

Nonindigenous species (NIS) can pose a threat to native species (Bax et al, 2003) by competing for food and space, which potentially can lead to eradication of the native species from their natural habitat (Blackburn et al, 2019; Karlson et al, 2007), but can act as predators or parasites on native species, be vectors of parasites, result in critical modifications of the habitat, hybridize with native species, change inherent biodiversity in the area, or be of economic consequences to human agriculture, industries and disrupt wildlife conservation plans (Behrens et al, 2017; Simberloff, 2003; Sherpa and Després, 2021). If native marine species and habitats are to be conserved by removing threats posed by NIS, a first step is to monitor the extent and dynamics of the distribution of the NIS (Ojaveer et al, 2017). This is especially challenging in cases including multiple and taxonomic different species, as monitoring efforts often will involve various types of field gear and sampling techniques. Such efforts will increase field expenses and potential response time, due to limited availability of needed taxonomic experts to identify the specimens collected. Comparing qPCR with metabarcoding there are at least four major differences:

Objectives

Methods

Discussion

Conclusion