The sceptical optimist: challenges and perspectives for the application of environmental DNA in marine fisheries

Abstract

Application of environmental DNA (eDNA) analysis has attracted the attention of researchers, advisors and managers of living marine resources and biodiversity. The apparent simplicity and cost‐effectiveness of eDNA analysis make it highly attractive as species distributions can be revealed from water samples. Further, species‐specific analyses indicate that eDNA concentrations correlate with biomass and abundance, suggesting the possibility for quantitative applications estimating abundance and biomass of specific organisms in marine ecosystems, such as for stock assessment. However, the path from detecting occurrence of an organism to quantitative estimates is long and indirect, not least as eDNA concentration depends on several physical, chemical and biological factors which influence its production, persistence and transport in marine ecosystems. Here, we provide an overview of basic principles in relation to eDNA analysis with potential for marine fisheries application. We describe fundamental processes governing eDNA generation, breakdown and transport and summarize current uncertainties about these processes. We describe five major challenges in relation to application in fisheries assessment, where there is immediate need for knowledge building in marine systems, and point to apparent weaknesses of eDNA compared to established marine fisheries monitoring methods. We provide an overview of emerging applications of interest to fisheries management and point to recent technological advances, which could improve analysis efficiency. We advise precaution against exaggerating the present scope for application of eDNA analysis in fisheries monitoring, but also argue that with informed insights into strengths and limitations, eDNA analysis can become an integrated tool in fisheries assessment and management.

False‐negative detections from environmental DNA collected in the presence of large numbers of killer whales (Orcinus orca)

“…We support current recommendations that advise pilot studies be performed on new systems/organisms before implementing eDNA monitoring (Hansen, Bekkevold, Clausen, & Nielsen, 2018;Harper et al, 2018), and furthermore, we encourage the publication of unsuccessful eDNA studies to better inform the eDNA research community, reduce financial and time losses due to ineffective study designs, and thereby aid the continued success of eDNA applications in future studies. Undoubtedly, eDNA has great potential in the context of cetacean monitoring and management, but as a complimentary additional tool rather than an outright replacement of tried and tested techniques.…”

Environmental DNA (eDNA) metabarcoding reveals strong discrimination among diverse marine habitats connected by water movement

“…The significant water displacement at our study site (Old & Vennell, ), however, could cause dilution rates to occur that lower DNA concentrations of a particular source rapidly beyond the limit of detection (Thomsen et al, ). Also, it has been posited that coastal regions might be less affected by eDNA transport, due to coastal morphology or retentive properties of seaweed (Hansen et al, ). Further investigation into the differences between coastal and offshore environments is therefore needed.…”

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

“…Community composition is expected to differ between sampling media, as previous eDNA studies have found sediment to show a higher DNA concentration and a longer detectability than surface water (Turner et al, 2015). Since DNA can persist longer when incorporated into the sediment, temporal inference may be challenging (Turner et al, 2015); on the other hand, a higher degradation rate and lower detection lag time in aqueous eDNA samples provide a contemporary snapshot of the biodiversity being assessed (Hansen et al, 2018). Here, we have found a significant difference (p < 0.05) and a higher size effect (R 2 = 0.06-0.08) on MOTU recovery between sediment and water samples ( (Shogren et al, 2017).…”