Full length articleLife in a drop: Sampling environmental DNA for marine fishery management and ecosystem monitoring
Introduction
Globally, it is increasingly acknowledged that our future depends on the maintenance of good environmental status and the conservation of biodiversity, both within defined regional and global standards [1], [2]. The broad consensus is endorsed by such global initiatives as the UN Sustainable Development Goals [3]. Moreover, international and national policies and legislation require the protection of the environment and ecosystems [4], [5], [6]. For example, this is explicitly aimed at under the remit of the development of an international instrument on marine biodiversity in areas beyond national jurisdiction (ABNJ) and stipulated in the European Union Marine Strategy Framework Directive [7], and also the Common Fisheries Policy (CFP). The implementation of such legal requirements requires commitment of the member states to carry out extensive monitoring in time and space, preferably in real-time. The development of tools to assess impacts such as invasive species introduction and spread, climate change, contaminants, eutrophication, fishing activities and marine litter on populations and ecosystem interactions remains a high priority. This is an increasingly challenging undertaking, to which state-of-the-art technological and scientific developments can and should contribute.
Effective ecosystem monitoring, the sustainable exploitation of aquatic living resources, sustainable fisheries management and associated policy development should be, as in the case of the CFP, a legally enshrined requirement, based on the best available scientific advice. The integration of scientific advice into governance and policy development and implementation is often challenging, particularly the communication of scientific approaches from specialists to managers and policy makers in a rapidly developing and specialised field. This review seeks to address this issue with regards to new genetic based techniques in the fields of species identification and community characterisation and thus facilitate more effective development of marine fishery management and monitoring approaches.
Effective fishery and ecosystem management rely on the identification and quantification of the species living a certain environment, that is, characterising its biodiversity. There are two significant limitations in gathering such information using traditional techniques: how to representatively sample the biodiversity in an ecosystem and how to identify individuals to species level? Sampling requires complicated logistics, is costly, is biased in its sampling coverage, and is especially difficult for species with low abundance and/or elusive species. Identification also requires taxonomic expertise, which is often lacking and difficult to apply in some cryptic species. The requirement to overcome such impediments has stimulated the search for new tools and approaches to integrate the various environmental dimensions in decision making into an evidence-based policy approach [8]. One such approach is utilisation of DNA collected from the environment to identify and/or quantify the species present in the ecosystem.
Environmental DNA (eDNA) stems from individual organisms which release DNA into the environment through waste products, skin/tissue, scales, gametes, mucus, blood and carcasses [9], [10], [11], [12]. This extra-organismal DNA is termed environmental DNA (eDNA) [13]. In contrast to DNA extracted from tissue samples, or community DNA – where DNA is extracted from communities of whole organisms - eDNA does not require sampling the target organisms themselves, but instead the sampling of the environment they live in [14], [15]. The development of new ways of monitoring marine ecosystems and marine biodiversity using eDNA has advanced over recent years and has revolutionised the ability to track invasive species, monitor endangered species, assess the health of fish stocks, and explore the world of marine biodiversity [16]. The seeming simplicity and cost-effectiveness of eDNA-based approaches, together with the interest from wider stakeholder groups, has made such applications highly attractive [17].
The development of genetic technologies to identify species and characterise whole communities through the collection and filtration of water and/or sediment sample is both a potentially invaluable tool for managers and an irresistible story for the popular press. Press articles focusing on such tools range from the very small, such as “New Nano Strategy Fights Superbugs” [18], to the very large (and improbable) “Loch Ness Monster Hunters to Try DNA Search?” [19]. Disentangling fact from fiction, and hyperbola from reality, is thus not a simple task for the manager striving to understand the field. As such this raises two opposing issues which could each negatively affect the ability to manage fisheries and monitor ecosystems using the most appropriate available scientific tools: the pre-emptive uptake of unproven approaches versus the failure to take advantage of robust new techniques. Stories in the press, together with questions from stakeholders, about new potential approaches that have been developed are often powerful incentives for major funding and uptake of these tools in practice [20]. Whilst in some cases this uptake may be justified, in others, especially in rapidly developing fields, such reliance may be potentially premature. However, each investment requires an accessible, robust and balanced evidence base as deriving management decisions on unproven and/or unreliable techniques brings obvious dangers and potential lack of trust in novel molecular technologies. Further, focusing effort and especially funding on such approaches means that other, perhaps more proven techniques with higher TRL (technology readiness levels) will be starved of resources. It is thus of particular importance that managers and policy makers can distinguish with confidence among approaches that although show promise, are at an early stage of validation.
The converse of the dangers of using unproven tools is avoiding the utilisation of effective proven tools due to uncertainties about their efficacy. As scientific technologies develop it is often the case that some areas progress further and faster than others. Proven approaches emerge and begin to be utilised in limited applications. In order to take full advantage of such developments in a wider context, managers need a straightforward guideline explaining the potential of each molecular tool and its state of readiness for routine applications in order to navigate in the various information streams and stakeholder drivers they are exposed to.
In order to bridge the information gap between the specialist and the manager, we provide here a non-technical synthesis of the evidence surrounding the use of eDNA based monitoring techniques for management of fisheries and ecosystems in the marine environment. It is not intended to be an exhaustive overview of the growing number of studies that have been carried out. Indeed, there are other reviews which attempt to do this [13], [17], [21], [22], [23]. Rather, we focus on key areas of interest, encompassing an overview of approaches with practical applications and priority needs. The focus here will be (i) to cover the different areas of interest to managers, (ii) to provide a brief overview of eDNA-based methods and strategies and (iii) to outline their state of development, practical uses, and development requirements, together with their limitations and factors which need to be addressed when integrating these tools into the management of marine resources.
Section snippets
Environmental DNA in a fisheries context
The marine environment harbours a huge diversity of species [24], ranging from large and charismatic whales to tiny worms and unicellular plankton (Fig. 1). Compared to the sampling of eDNA in freshwater it also poses its own set of, often difficult to address, issues when trying to obtain unbiased samples, especially in relation to factors such, tides, currents, great depths and rapid movements of individuals in three dimensions. Thus, depending on the habitat and taxa of interest, various
From water to results - the eDNA workflow and approaches
Identifying the presence of a particular species or characterizing the entire community from eDNA samples requires a series of steps that often need to be adjusted to each case study and fully understood in order to derive sound conclusions from the data obtained [30]. Sampling eDNA in the marine environment is possible through water or sediment [31]. It is however usually done by collecting water that is subsequently passed through variable pore size filters, generally <1 µm pore size. It is
Considerations
Analysis of eDNA allows inferences to be made about organisms, without the need to see, observe or handle them. This is the major advantage offered by this approach, but also potentially a drawback. In order to make the most informed decisions and use eDNA approaches to their fullest, managers and policy makers should be aware of the issues to be considered when seeking to understand the results of eDNA surveys. Although eDNA based applications are relatively new, especially in the context of
Integration into existing management and monitoring programmes
The development of new approaches to gather information of relevance to fisheries and ecosystem monitoring through the use of eDNA sampling methods, and the associated novel insights such approaches generate, has the potential to revolutionise the information available to managers. However, together with the requirement for the new methods to be able to provide robust results, there is also a need to investigate the practicalities and cost-benefit of incorporating the new techniques into
Conclusion
Rapid developments in the field of eDNA analysis have provided a range of new tools for research scientists, and fishery and ecosystem managers. With such developments, it is not straightforward for the manager to disentangle which tools can provide robust evidence to incorporate into policy development discussions, and which are still in the developmental phase. In tandem, reports about such advances in the mainstream media drive stakeholders to question managers about the utility of the
CRediT authorship contribution statement
JG led the ICES WGAGFA Terms of Reference on eDNA in Fisheries Management and Ecosystem Monitoring which resulted in the production of the manuscript. JG took the lead in writing the manuscript. All authors were involved in discussions and decisions to shape the manuscript and contributed to the writing of the final text.
Declarations of interest
None.
Acknowledgments
This review is the result of discussion within the ICES Working Group on the Application of Genetics in Fisheries and Aquaculture (ICES-WGAGFA) and the authors wish to thank members for a most stimulating scientific environment. NRE’s contribution has been funded by the Spanish Ministry of Science, Innovation and Universities through the EDAMAME ("Environmental DNA based approaches for marine and aquatic monitoring and evaluation") project (code CTM2017-89500-R). FAMV acknowledges the
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2023, Biological ConservationCitation Excerpt :Methods of species detection using eDNA are non-invasive, cost-effective and have remarkable efficiencies, with a recent meta-analysis revealing eDNA surveys outperform traditional surveys (Fediajevaite et al., 2021). Due to these attributes, eDNA surveys are predicted to revolutionise contemporary marine biodiversity monitoring (see Gilbey et al., 2021 for recent review). Despite the potential utility to advance species detection and biodiversity assessments, the use of eDNA in applied environmental monitoring has been largely underexploited (see Langlois et al., 2021 for further discussion).